Restriction enzyme and siRNA technologies exist for site-specific knockout of genes. These two technologies are limited to one kind of targeted molecule. The presently described system is more flexible and provides an alternative method for directing the site-specific modification of nucleic acids, particularly DNA.
Aside from the common double helix, DNA forms a wide range of structural motifs, such as hairpin loops, triplex, tetraplex, bulged structures, as well as nicks and gaps. The individual structural features of these motifs make them potential candidates for specific targeting. Among these structural elements, nicks and gaps are promising for the development of sequence-specific DNA cleavage, since they already feature a break in the phosphate backbone of DNA.
Cleavage of the phosphate backbone of DNA can be caused by chemical reagents such as radicals and by radiation damage. In order to survive, cells developed enzymatic mechanisms for the repair which work efficiently on single strand (ss) damage. Any further cleavage on the opposite strand at the damage site leads to double stranded (ds) cleavage, which is hard to repair. Ds cleavage requires either a bifunctional reagent or detection and targeting of the damaged site. The only literature example of the latter is a complex natural antibiotic, bleomycin.